Analysis of bla_SHV-12-carrying Escherichia coli clones and plasmids from human, animal and food sources

Objectives: This study aimed at characterizing 23 Escherichia coli isolates from various sources and their respective blaSHV-12-carrying plasmids and sequencing one of these plasmids completely. Methods: Isolates were typed by XbaI-PFGE, MLST and PCR-based phylotyping. Transformed blaSHV-12-carrying plasmids were examined by replicon typing, S1-nuclease, conjugation, EcoRI-HindIII-BamHI digests and plasmid MLST. Co-located resistance genes and integrons as well as the blaSHV-12 genetic environment were analysed by PCR and sequencing. One IncI1 plasmid was sequenced completely using HiSeq 2500 and gap closure by PCRs and Sanger sequencing. Results: Among the 23 SHV-12-positive E. coli, some isolates from different sources showed the same characteristics: ST23/phylogroup A (human, dog, livestock), ST57/D (wild bird, chicken meat) and ST117/D (chicken meat, chicken). All blaSHV-12 genes were horizontally transferable via 30–120 kb plasmids of incompatibility groups IncI1 (n = 17), IncK (n = 3), IncF (n = 1), IncX3 (n = 1) and a non-typeable plasmid. IncK plasmids, indistinguishable in size and restriction patterns, were found in isolates from different sources (ST57/D, meat; ST131/B2, meat; ST57/B1, dog). The IncI1-blaSHV-12-carrying plasmids were mostly assigned to plasmid ST (pST) 26 and pST3. Three plasmids showed novel pSTs (pST214, pST215). The majority of the IncI1 transformants exhibited resistance to β-lactams, chloramphenicol and streptomycin (in relation with a class 1 integron containing an estX-psp-aadA2-cmlA1-aadA1-qacI gene cassette array), and to tetracycline. A novel blaSHV-12 environment was detected and whole plasmid sequencing revealed a Tn21-derived-blaSHV12-ΔTn1721 resistance complex. Conclusions: Results from this study suggest that the dissemination of blaSHV-12 genes occurs by vertical (clonal) and horizontal transfer, the latter mainly mediated through IncI1 multidrug-resistance plasmids.